Starting phenix.real_space_refine on Sat Aug 23 17:45:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ysr_34081/08_2025/7ysr_34081.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ysr_34081/08_2025/7ysr_34081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ysr_34081/08_2025/7ysr_34081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ysr_34081/08_2025/7ysr_34081.map" model { file = "/net/cci-nas-00/data/ceres_data/7ysr_34081/08_2025/7ysr_34081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ysr_34081/08_2025/7ysr_34081.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 98 5.16 5 C 8462 2.51 5 N 2298 2.21 5 O 2586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13456 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3314 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3350 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "C" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3314 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Chain: "D" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3350 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.67, per 1000 atoms: 0.20 Number of scatterers: 13456 At special positions: 0 Unit cell: (112.32, 109.08, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 12 15.00 O 2586 8.00 N 2298 7.00 C 8462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 433.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 54.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.767A pdb=" N VAL A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.967A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 128 removed outlier: 5.842A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 removed outlier: 4.421A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.503A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.812A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.583A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 4.026A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 382 through 398 removed outlier: 4.117A pdb=" N GLU A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.817A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.883A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 40 through 48 removed outlier: 4.106A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 129 removed outlier: 4.055A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 removed outlier: 3.853A pdb=" N SER B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 4.043A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 223 through 244 removed outlier: 4.467A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.686A pdb=" N GLN B 282 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG B 284 " --> pdb=" O GLN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.928A pdb=" N GLN B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.548A pdb=" N MET B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 382 through 398 removed outlier: 4.190A pdb=" N GLU B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 removed outlier: 4.415A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 435 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 71 through 80 removed outlier: 4.854A pdb=" N VAL C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 128 removed outlier: 5.711A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 118 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 162 removed outlier: 4.360A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.546A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 217 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.690A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.785A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 382 through 398 removed outlier: 3.912A pdb=" N GLU C 386 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.772A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 3.939A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 40 through 48 removed outlier: 4.029A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.803A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D 76 " --> pdb=" O PRO D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 110 through 129 removed outlier: 4.176A pdb=" N LEU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 removed outlier: 3.752A pdb=" N SER D 147 " --> pdb=" O GLY D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 4.537A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 223 through 244 removed outlier: 4.504A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 279 through 284 removed outlier: 4.031A pdb=" N ARG D 284 " --> pdb=" O GLN D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 382 through 400 removed outlier: 4.205A pdb=" N GLU D 386 " --> pdb=" O THR D 382 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 removed outlier: 4.440A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 435 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.539A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N SER A 140 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL A 9 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 4.039A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.821A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASN A 356 " --> pdb=" O MET A 317 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.039A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 5 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 165 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.846A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 68 removed outlier: 8.662A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE C 171 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.979A pdb=" N LYS C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 removed outlier: 6.501A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS C 376 " --> pdb=" O MET C 317 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N LYS C 352 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS C 315 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLY C 354 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 317 " --> pdb=" O GLY C 354 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN C 356 " --> pdb=" O MET C 317 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR C 319 " --> pdb=" O ASN C 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 93 through 94 removed outlier: 8.013A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS D 6 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLU D 3 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER D 140 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N TYR D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU D 137 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 56 648 hydrogen bonds defined for protein. 1857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4452 1.34 - 1.46: 3244 1.46 - 1.58: 5894 1.58 - 1.70: 22 1.70 - 1.82: 152 Bond restraints: 13764 Sorted by residual: bond pdb=" C ARG A 320 " pdb=" N GLY A 321 " ideal model delta sigma weight residual 1.334 1.322 0.012 1.12e-02 7.97e+03 1.20e+00 bond pdb=" CB LYS D 124 " pdb=" CG LYS D 124 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.64e-01 bond pdb=" C VAL D 62 " pdb=" O VAL D 62 " ideal model delta sigma weight residual 1.232 1.241 -0.008 8.90e-03 1.26e+04 8.62e-01 bond pdb=" CA ILE C 171 " pdb=" CB ILE C 171 " ideal model delta sigma weight residual 1.527 1.538 -0.012 1.31e-02 5.83e+03 7.94e-01 bond pdb=" C SER B 324 " pdb=" N MET B 325 " ideal model delta sigma weight residual 1.333 1.320 0.013 1.56e-02 4.11e+03 7.24e-01 ... (remaining 13759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 18252 1.61 - 3.22: 371 3.22 - 4.83: 45 4.83 - 6.44: 16 6.44 - 8.05: 10 Bond angle restraints: 18694 Sorted by residual: angle pdb=" CA MET B 325 " pdb=" C MET B 325 " pdb=" N LYS B 326 " ideal model delta sigma weight residual 118.59 123.67 -5.08 1.63e+00 3.76e-01 9.72e+00 angle pdb=" C ARG C 214 " pdb=" N ARG C 215 " pdb=" CA ARG C 215 " ideal model delta sigma weight residual 122.60 117.90 4.70 1.56e+00 4.11e-01 9.06e+00 angle pdb=" CA MET A 317 " pdb=" CB MET A 317 " pdb=" CG MET A 317 " ideal model delta sigma weight residual 114.10 119.73 -5.63 2.00e+00 2.50e-01 7.92e+00 angle pdb=" CB MET A 317 " pdb=" CG MET A 317 " pdb=" SD MET A 317 " ideal model delta sigma weight residual 112.70 120.75 -8.05 3.00e+00 1.11e-01 7.21e+00 angle pdb=" CB MET D 332 " pdb=" CG MET D 332 " pdb=" SD MET D 332 " ideal model delta sigma weight residual 112.70 120.58 -7.88 3.00e+00 1.11e-01 6.90e+00 ... (remaining 18689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 8019 35.37 - 70.74: 142 70.74 - 106.12: 11 106.12 - 141.49: 3 141.49 - 176.86: 1 Dihedral angle restraints: 8176 sinusoidal: 3280 harmonic: 4896 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -113.87 -176.86 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -157.88 -132.85 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -11.36 115.95 1 2.00e+01 2.50e-03 3.45e+01 ... (remaining 8173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1346 0.036 - 0.072: 474 0.072 - 0.109: 175 0.109 - 0.145: 43 0.145 - 0.181: 4 Chirality restraints: 2042 Sorted by residual: chirality pdb=" CB ILE D 318 " pdb=" CA ILE D 318 " pdb=" CG1 ILE D 318 " pdb=" CG2 ILE D 318 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CB THR D 221 " pdb=" CA THR D 221 " pdb=" OG1 THR D 221 " pdb=" CG2 THR D 221 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB THR B 221 " pdb=" CA THR B 221 " pdb=" OG1 THR B 221 " pdb=" CG2 THR B 221 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 2039 not shown) Planarity restraints: 2426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 389 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C LYS B 389 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS B 389 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 390 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 89 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 123 " 0.130 9.50e-02 1.11e+02 5.83e-02 2.14e+00 pdb=" NE ARG A 123 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 123 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 123 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 123 " 0.006 2.00e-02 2.50e+03 ... (remaining 2423 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 359 2.69 - 3.25: 14507 3.25 - 3.80: 23270 3.80 - 4.35: 28990 4.35 - 4.90: 47830 Nonbonded interactions: 114956 Sorted by model distance: nonbonded pdb=" OH TYR B 185 " pdb=" O MET B 398 " model vdw 2.142 3.040 nonbonded pdb=" OH TYR D 185 " pdb=" O MET D 398 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR C 185 " pdb=" O MET C 398 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR A 185 " pdb=" O MET A 398 " model vdw 2.166 3.040 nonbonded pdb=" NH1 ARG C 215 " pdb=" OD1 ASN C 216 " model vdw 2.173 3.120 ... (remaining 114951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.350 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13764 Z= 0.142 Angle : 0.590 8.053 18694 Z= 0.308 Chirality : 0.043 0.181 2042 Planarity : 0.004 0.058 2426 Dihedral : 14.906 176.861 5040 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.21), residues: 1684 helix: 1.05 (0.19), residues: 746 sheet: 0.30 (0.32), residues: 280 loop : -0.36 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 123 TYR 0.021 0.001 TYR C 224 PHE 0.013 0.001 PHE B 377 TRP 0.019 0.001 TRP C 21 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00293 (13764) covalent geometry : angle 0.58959 (18694) hydrogen bonds : bond 0.14725 ( 648) hydrogen bonds : angle 6.13991 ( 1857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 325 MET cc_start: 0.8338 (ptt) cc_final: 0.7980 (ptt) REVERT: D 124 LYS cc_start: 0.9584 (tmtt) cc_final: 0.9362 (tptp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0987 time to fit residues: 19.0919 Evaluate side-chains 95 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 8.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 206 ASN B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.052866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045792 restraints weight = 75637.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.047109 restraints weight = 44747.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048051 restraints weight = 30621.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.048736 restraints weight = 22966.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.049247 restraints weight = 18294.765| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13764 Z= 0.112 Angle : 0.542 7.206 18694 Z= 0.278 Chirality : 0.043 0.161 2042 Planarity : 0.004 0.056 2426 Dihedral : 8.599 178.073 1902 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.21 % Allowed : 5.62 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.21), residues: 1684 helix: 1.42 (0.19), residues: 770 sheet: 0.50 (0.31), residues: 290 loop : -0.23 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 121 TYR 0.011 0.001 TYR A 282 PHE 0.009 0.001 PHE C 149 TRP 0.013 0.001 TRP C 21 HIS 0.008 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00235 (13764) covalent geometry : angle 0.54237 (18694) hydrogen bonds : bond 0.03782 ( 648) hydrogen bonds : angle 4.75800 ( 1857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8046 (t80) cc_final: 0.7557 (t80) REVERT: B 124 LYS cc_start: 0.9404 (tmtt) cc_final: 0.9204 (tptp) REVERT: B 325 MET cc_start: 0.8369 (ptt) cc_final: 0.8118 (ptt) REVERT: C 124 LYS cc_start: 0.8936 (pttm) cc_final: 0.8712 (pttm) REVERT: D 124 LYS cc_start: 0.9516 (tmtt) cc_final: 0.9276 (tptp) REVERT: D 299 LYS cc_start: 0.8545 (ptmm) cc_final: 0.8255 (tmmt) REVERT: D 301 MET cc_start: 0.8513 (mmm) cc_final: 0.8145 (mmp) REVERT: D 302 MET cc_start: 0.8583 (mtm) cc_final: 0.8267 (mtm) REVERT: D 413 MET cc_start: 0.8933 (mmm) cc_final: 0.8681 (mmp) outliers start: 3 outliers final: 0 residues processed: 134 average time/residue: 0.1073 time to fit residues: 20.8819 Evaluate side-chains 95 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 90 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 167 ASN D 192 HIS D 193 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.044169 restraints weight = 78709.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.045444 restraints weight = 47270.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.046370 restraints weight = 32470.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.047024 restraints weight = 24390.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.047522 restraints weight = 19620.340| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13764 Z= 0.227 Angle : 0.612 7.743 18694 Z= 0.314 Chirality : 0.044 0.189 2042 Planarity : 0.004 0.064 2426 Dihedral : 8.757 175.453 1902 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.20), residues: 1684 helix: 1.36 (0.18), residues: 766 sheet: 0.24 (0.31), residues: 282 loop : -0.27 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 121 TYR 0.024 0.002 TYR A 224 PHE 0.025 0.002 PHE B 214 TRP 0.013 0.001 TRP C 21 HIS 0.007 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00480 (13764) covalent geometry : angle 0.61220 (18694) hydrogen bonds : bond 0.03918 ( 648) hydrogen bonds : angle 4.78945 ( 1857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8131 (mpp) cc_final: 0.7833 (mpp) REVERT: B 124 LYS cc_start: 0.9438 (tmtt) cc_final: 0.9201 (tptp) REVERT: B 301 MET cc_start: 0.8394 (mmp) cc_final: 0.8086 (mmp) REVERT: B 325 MET cc_start: 0.8513 (ptt) cc_final: 0.8103 (ptt) REVERT: D 124 LYS cc_start: 0.9494 (tmtt) cc_final: 0.9259 (tptp) REVERT: D 295 MET cc_start: 0.8177 (tpt) cc_final: 0.7954 (tpp) REVERT: D 299 LYS cc_start: 0.8538 (ptmm) cc_final: 0.8237 (tmmt) REVERT: D 301 MET cc_start: 0.8594 (mmm) cc_final: 0.8214 (mmp) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.1140 time to fit residues: 20.6516 Evaluate side-chains 92 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.051822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.044694 restraints weight = 77325.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046032 restraints weight = 45427.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.046965 restraints weight = 30959.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.047621 restraints weight = 23275.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.048136 restraints weight = 18607.586| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13764 Z= 0.151 Angle : 0.569 7.517 18694 Z= 0.291 Chirality : 0.043 0.174 2042 Planarity : 0.004 0.063 2426 Dihedral : 8.700 174.015 1902 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.20), residues: 1684 helix: 1.36 (0.18), residues: 766 sheet: 0.25 (0.30), residues: 284 loop : -0.29 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 123 TYR 0.011 0.001 TYR A 224 PHE 0.012 0.001 PHE D 377 TRP 0.012 0.001 TRP C 21 HIS 0.012 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00323 (13764) covalent geometry : angle 0.56936 (18694) hydrogen bonds : bond 0.03606 ( 648) hydrogen bonds : angle 4.69417 ( 1857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8096 (mpp) cc_final: 0.7737 (mpp) REVERT: B 124 LYS cc_start: 0.9532 (tmtt) cc_final: 0.9164 (tptp) REVERT: B 301 MET cc_start: 0.8387 (mmp) cc_final: 0.8148 (mmp) REVERT: B 325 MET cc_start: 0.8605 (ptt) cc_final: 0.8140 (ptp) REVERT: C 154 MET cc_start: 0.8269 (ttt) cc_final: 0.8031 (ttt) REVERT: C 377 MET cc_start: 0.8503 (ppp) cc_final: 0.7834 (ppp) REVERT: D 124 LYS cc_start: 0.9469 (tmtt) cc_final: 0.9247 (tptp) REVERT: D 156 LYS cc_start: 0.9596 (mmmm) cc_final: 0.9387 (mmmm) REVERT: D 295 MET cc_start: 0.8229 (tpt) cc_final: 0.8023 (tpp) REVERT: D 299 LYS cc_start: 0.8965 (ptmm) cc_final: 0.8510 (tmmt) REVERT: D 301 MET cc_start: 0.8651 (mmm) cc_final: 0.8293 (mmp) REVERT: D 302 MET cc_start: 0.8629 (mtm) cc_final: 0.8198 (mtm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1292 time to fit residues: 24.0420 Evaluate side-chains 93 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 24 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.050657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.043736 restraints weight = 78525.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.044978 restraints weight = 46796.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045880 restraints weight = 32291.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.046516 restraints weight = 24324.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.046991 restraints weight = 19609.180| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13764 Z= 0.244 Angle : 0.636 8.047 18694 Z= 0.327 Chirality : 0.045 0.177 2042 Planarity : 0.004 0.071 2426 Dihedral : 8.872 171.358 1902 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.20), residues: 1684 helix: 1.18 (0.18), residues: 768 sheet: 0.03 (0.30), residues: 284 loop : -0.35 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 123 TYR 0.014 0.002 TYR B 61 PHE 0.014 0.002 PHE A 149 TRP 0.014 0.002 TRP A 21 HIS 0.009 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00517 (13764) covalent geometry : angle 0.63634 (18694) hydrogen bonds : bond 0.04007 ( 648) hydrogen bonds : angle 4.83886 ( 1857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8080 (mpp) cc_final: 0.7794 (mpp) REVERT: B 124 LYS cc_start: 0.9500 (tmtt) cc_final: 0.9160 (tptp) REVERT: B 301 MET cc_start: 0.8430 (mmp) cc_final: 0.8184 (mmp) REVERT: B 325 MET cc_start: 0.8721 (ptt) cc_final: 0.8241 (ptp) REVERT: C 154 MET cc_start: 0.8174 (ttt) cc_final: 0.7933 (ttt) REVERT: D 124 LYS cc_start: 0.9486 (tmtt) cc_final: 0.9269 (tptp) REVERT: D 295 MET cc_start: 0.8267 (tpt) cc_final: 0.7922 (tpp) REVERT: D 299 LYS cc_start: 0.8974 (ptmm) cc_final: 0.8492 (tmmt) REVERT: D 301 MET cc_start: 0.8694 (mmm) cc_final: 0.8179 (mmp) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1171 time to fit residues: 20.1038 Evaluate side-chains 90 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 119 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 7 optimal weight: 0.0050 chunk 139 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN C 283 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.052506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045405 restraints weight = 76053.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.046726 restraints weight = 44710.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.047681 restraints weight = 30348.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048360 restraints weight = 22644.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.048864 restraints weight = 18060.999| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13764 Z= 0.123 Angle : 0.583 8.662 18694 Z= 0.298 Chirality : 0.044 0.169 2042 Planarity : 0.003 0.032 2426 Dihedral : 8.713 169.904 1902 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.20), residues: 1684 helix: 1.18 (0.18), residues: 782 sheet: 0.28 (0.32), residues: 268 loop : -0.35 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 123 TYR 0.028 0.001 TYR C 282 PHE 0.012 0.001 PHE B 388 TRP 0.010 0.001 TRP A 21 HIS 0.008 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00267 (13764) covalent geometry : angle 0.58348 (18694) hydrogen bonds : bond 0.03690 ( 648) hydrogen bonds : angle 4.72886 ( 1857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.9199 (pptt) cc_final: 0.8995 (pptt) REVERT: A 313 MET cc_start: 0.8162 (mpp) cc_final: 0.7833 (mpp) REVERT: B 124 LYS cc_start: 0.9397 (tmtt) cc_final: 0.9135 (tptp) REVERT: B 301 MET cc_start: 0.8456 (mmp) cc_final: 0.8223 (mmp) REVERT: B 325 MET cc_start: 0.8704 (ptt) cc_final: 0.8207 (ptp) REVERT: D 124 LYS cc_start: 0.9468 (tmtt) cc_final: 0.9242 (tptp) REVERT: D 295 MET cc_start: 0.8287 (tpt) cc_final: 0.7941 (tpp) REVERT: D 299 LYS cc_start: 0.8925 (ptmm) cc_final: 0.8415 (tmmt) REVERT: D 301 MET cc_start: 0.8732 (mmm) cc_final: 0.8236 (mmp) REVERT: D 302 MET cc_start: 0.8649 (mtm) cc_final: 0.8298 (mtm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1190 time to fit residues: 21.9348 Evaluate side-chains 92 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 134 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 chunk 78 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 436 GLN C 283 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.051918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.044909 restraints weight = 77053.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.046181 restraints weight = 45937.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.047100 restraints weight = 31570.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047748 restraints weight = 23814.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048228 restraints weight = 19131.448| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13764 Z= 0.149 Angle : 0.583 7.577 18694 Z= 0.297 Chirality : 0.044 0.175 2042 Planarity : 0.003 0.027 2426 Dihedral : 8.688 168.129 1902 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.20), residues: 1684 helix: 1.23 (0.18), residues: 782 sheet: 0.23 (0.31), residues: 270 loop : -0.40 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 123 TYR 0.018 0.001 TYR C 224 PHE 0.011 0.001 PHE C 149 TRP 0.009 0.001 TRP A 21 HIS 0.007 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00327 (13764) covalent geometry : angle 0.58259 (18694) hydrogen bonds : bond 0.03666 ( 648) hydrogen bonds : angle 4.67187 ( 1857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.9209 (pptt) cc_final: 0.8988 (pptt) REVERT: A 313 MET cc_start: 0.8109 (mpp) cc_final: 0.7786 (mpp) REVERT: B 124 LYS cc_start: 0.9404 (tmtt) cc_final: 0.9171 (tptp) REVERT: B 156 LYS cc_start: 0.9183 (mmmt) cc_final: 0.8646 (mmmm) REVERT: B 159 GLU cc_start: 0.8563 (pp20) cc_final: 0.8142 (pp20) REVERT: B 301 MET cc_start: 0.8436 (mmp) cc_final: 0.8209 (mmp) REVERT: B 325 MET cc_start: 0.8479 (ptp) cc_final: 0.7998 (ptp) REVERT: C 377 MET cc_start: 0.8473 (ppp) cc_final: 0.8183 (ppp) REVERT: D 124 LYS cc_start: 0.9454 (tmtt) cc_final: 0.9245 (tptp) REVERT: D 295 MET cc_start: 0.8311 (tpt) cc_final: 0.7922 (tpp) REVERT: D 299 LYS cc_start: 0.8942 (ptmm) cc_final: 0.8396 (ttpp) REVERT: D 301 MET cc_start: 0.8718 (mmm) cc_final: 0.8155 (mmp) REVERT: D 302 MET cc_start: 0.8704 (mtm) cc_final: 0.8311 (mtm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1111 time to fit residues: 20.6875 Evaluate side-chains 92 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 153 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 28 optimal weight: 0.1980 chunk 163 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.051080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.044126 restraints weight = 77100.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.045371 restraints weight = 46137.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.046273 restraints weight = 31842.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.046881 restraints weight = 24099.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.047370 restraints weight = 19527.774| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13764 Z= 0.220 Angle : 0.640 8.132 18694 Z= 0.330 Chirality : 0.045 0.164 2042 Planarity : 0.004 0.031 2426 Dihedral : 8.770 166.061 1902 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.20), residues: 1684 helix: 1.11 (0.18), residues: 782 sheet: 0.07 (0.31), residues: 270 loop : -0.45 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 123 TYR 0.017 0.001 TYR C 224 PHE 0.028 0.002 PHE C 135 TRP 0.010 0.001 TRP A 21 HIS 0.008 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00470 (13764) covalent geometry : angle 0.63985 (18694) hydrogen bonds : bond 0.03861 ( 648) hydrogen bonds : angle 4.96593 ( 1857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.9259 (pptt) cc_final: 0.9015 (pptt) REVERT: A 313 MET cc_start: 0.8069 (mpp) cc_final: 0.7563 (mpp) REVERT: B 124 LYS cc_start: 0.9406 (tmtt) cc_final: 0.9167 (tptp) REVERT: B 301 MET cc_start: 0.8433 (mmp) cc_final: 0.8220 (mmp) REVERT: B 325 MET cc_start: 0.8492 (ptp) cc_final: 0.8027 (ptp) REVERT: D 124 LYS cc_start: 0.9465 (tmtt) cc_final: 0.9256 (tptp) REVERT: D 295 MET cc_start: 0.8398 (tpt) cc_final: 0.7979 (tpp) REVERT: D 299 LYS cc_start: 0.8946 (ptmm) cc_final: 0.8393 (ttpp) REVERT: D 302 MET cc_start: 0.8692 (mtm) cc_final: 0.8257 (mtm) REVERT: D 329 ASP cc_start: 0.9338 (m-30) cc_final: 0.9081 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1097 time to fit residues: 18.9265 Evaluate side-chains 93 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 85 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 82 optimal weight: 0.0040 chunk 161 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.052056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.044867 restraints weight = 77473.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046164 restraints weight = 45527.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047087 restraints weight = 31222.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.047751 restraints weight = 23639.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048246 restraints weight = 18981.194| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13764 Z= 0.155 Angle : 0.614 10.270 18694 Z= 0.311 Chirality : 0.045 0.195 2042 Planarity : 0.004 0.038 2426 Dihedral : 8.686 164.102 1902 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.07 % Allowed : 0.62 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.20), residues: 1684 helix: 1.10 (0.18), residues: 784 sheet: 0.05 (0.31), residues: 268 loop : -0.45 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 123 TYR 0.017 0.001 TYR C 282 PHE 0.018 0.001 PHE C 135 TRP 0.009 0.001 TRP C 21 HIS 0.007 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00336 (13764) covalent geometry : angle 0.61355 (18694) hydrogen bonds : bond 0.03768 ( 648) hydrogen bonds : angle 4.85245 ( 1857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.9233 (pptt) cc_final: 0.8968 (pptt) REVERT: A 313 MET cc_start: 0.8077 (mpp) cc_final: 0.7762 (mpp) REVERT: A 377 MET cc_start: 0.8361 (ppp) cc_final: 0.8009 (ppp) REVERT: B 124 LYS cc_start: 0.9414 (tmtt) cc_final: 0.9181 (tptp) REVERT: B 301 MET cc_start: 0.8398 (mmp) cc_final: 0.8178 (mmp) REVERT: B 325 MET cc_start: 0.8549 (ptp) cc_final: 0.8039 (ptp) REVERT: D 124 LYS cc_start: 0.9445 (tmtt) cc_final: 0.9244 (tptp) REVERT: D 295 MET cc_start: 0.8372 (tpt) cc_final: 0.8026 (tpp) REVERT: D 299 LYS cc_start: 0.8940 (ptmm) cc_final: 0.8359 (ttpp) REVERT: D 302 MET cc_start: 0.8775 (mtm) cc_final: 0.8312 (mtm) REVERT: D 336 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7628 (tp-100) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.0973 time to fit residues: 17.7459 Evaluate side-chains 91 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044902 restraints weight = 76796.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.046208 restraints weight = 45369.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.047138 restraints weight = 31008.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047789 restraints weight = 23447.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.048269 restraints weight = 18820.008| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13764 Z= 0.149 Angle : 0.619 8.851 18694 Z= 0.313 Chirality : 0.044 0.188 2042 Planarity : 0.004 0.042 2426 Dihedral : 8.638 161.765 1902 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.20), residues: 1684 helix: 1.13 (0.18), residues: 782 sheet: 0.05 (0.31), residues: 270 loop : -0.45 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 123 TYR 0.013 0.001 TYR C 224 PHE 0.016 0.001 PHE C 135 TRP 0.009 0.001 TRP B 21 HIS 0.007 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00327 (13764) covalent geometry : angle 0.61869 (18694) hydrogen bonds : bond 0.03736 ( 648) hydrogen bonds : angle 4.81611 ( 1857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8071 (mpp) cc_final: 0.7703 (mpp) REVERT: A 377 MET cc_start: 0.8332 (ppp) cc_final: 0.7802 (ppp) REVERT: B 124 LYS cc_start: 0.9416 (tmtt) cc_final: 0.9185 (tptp) REVERT: B 156 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8668 (mmmm) REVERT: B 159 GLU cc_start: 0.8596 (pp20) cc_final: 0.8136 (pp20) REVERT: B 301 MET cc_start: 0.8419 (mmp) cc_final: 0.8153 (mmp) REVERT: B 325 MET cc_start: 0.8567 (ptp) cc_final: 0.8040 (ptp) REVERT: C 377 MET cc_start: 0.8469 (ppp) cc_final: 0.7280 (ppp) REVERT: D 124 LYS cc_start: 0.9438 (tmtt) cc_final: 0.9235 (tptp) REVERT: D 295 MET cc_start: 0.8348 (tpt) cc_final: 0.7938 (tpp) REVERT: D 299 LYS cc_start: 0.8946 (ptmm) cc_final: 0.8328 (tmmt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1163 time to fit residues: 20.4292 Evaluate side-chains 92 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.052414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045241 restraints weight = 76659.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.046557 restraints weight = 45701.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.047483 restraints weight = 31332.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.048156 restraints weight = 23659.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048640 restraints weight = 18997.800| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13764 Z= 0.119 Angle : 0.598 8.582 18694 Z= 0.303 Chirality : 0.044 0.191 2042 Planarity : 0.003 0.039 2426 Dihedral : 8.542 158.645 1902 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.20), residues: 1684 helix: 1.22 (0.18), residues: 782 sheet: 0.07 (0.30), residues: 278 loop : -0.47 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 123 TYR 0.017 0.001 TYR C 282 PHE 0.013 0.001 PHE C 135 TRP 0.009 0.001 TRP A 346 HIS 0.007 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00262 (13764) covalent geometry : angle 0.59763 (18694) hydrogen bonds : bond 0.03638 ( 648) hydrogen bonds : angle 4.71452 ( 1857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1653.21 seconds wall clock time: 29 minutes 49.54 seconds (1789.54 seconds total)